chr2-135728401-T-C

Position:

• chr2-135728401-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.306 in 152,032 control chromosomes in the GnomAD database, including 9,233 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.31 (9233 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0290

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.512 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.306 AC: 46422 AN: 151914 Hom.: 9212 Cov.: 32

Gnomad AFR AF: 0.518

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.481

Gnomad EAS AF: 0.500

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.343

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.306 AC: 46509 AN: 152032 Hom.: 9233 Cov.: 32 AF XY: 0.306 AC XY: 22736 AN XY: 74308

Gnomad4 AFR AF: 0.518

Gnomad4 AMR AF: 0.319

Gnomad4 ASJ AF: 0.481

Gnomad4 EAS AF: 0.501

Gnomad4 SAS AF: 0.295

Gnomad4 FIN AF: 0.154

Gnomad4 NFE AF: 0.175

Gnomad4 OTH AF: 0.348

Alfa AF: 0.224 Hom.: 4112

Bravo AF: 0.329

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.2
DANN	Benign	0.53

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs724326; hg19: chr2-136485971;